Summary of Study ST002008

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001273. The data can be accessed directly via it's Project DOI: 10.21228/M85D8M This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002008
Study TitleGlycine betaine uptake and metabolism in marine microbial communities
Study TypeQuantitative and qualitative exploration of isotope-labeled glycine betaine uptake and use in natural marine microbial communities
Study SummaryGlycine betaine (GBT) is a component of labile dissolved organic matter and a compatible solute in high concentrations in marine microbial populations. GBT has complex biochemical potential, but, once taken up from the environment, the cellular fate of the carbon and nitrogen from GBT is unknown. Here we determine the uptake kinetics and metabolism of GBT in two natural microbial communities characterized by different nitrate concentrations in the North Pacific transition zone. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM hr -1 and half-saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations, respectively. GBT taken into cells was predominantly retained as an untransformed compatible solute. A portion of GBT was transformed into other metabolites, through characterized and uncharacterized pathways. Where nitrate was scarce, GBT was primarily catabolized via the demethylation to glycine. Resulting metabolites were used to build protein biomass, and remineralized ammonia was re-assimilated into cells. Gene expression data from this region show that bacteria, especially SAR11, are the dominant organisms expressing the demethylation genes. Where nitrate concentrations were higher, more GBT was used for choline synthesis. Our data highlight undiscussed metabolic pathways and potential routes of microbial metabolite exchange.
Institute
University of Washington
DepartmentSchool of Oceanography
LaboratoryIngalls Lab
Last NameKumler
First NameWilliam
Address1501 NE Boat St, Seattle, WA 98105
Emailwkumler@uw.edu
Phone2062216732
Submit Date2021-12-01
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Waters)
Analysis Type DetailLC-MS
Release Date2022-01-17
Release Version1
William Kumler William Kumler
https://dx.doi.org/10.21228/M85D8M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001273
Project DOI:doi: 10.21228/M85D8M
Project Title:Glycine betaine uptake and metabolism in marine microbial communities
Project Type:Marine Metabolomics
Project Summary:Glycine betaine (GBT) is a component of labile dissolved organic matter and a compatible solute in high concentrations in marine microbial populations. GBT has complex biochemical potential, but, once taken up from the environment, the cellular fate of the carbon and nitrogen from GBT is unknown. Here we determine the uptake kinetics and metabolism of GBT in two natural microbial communities characterized by different nitrate concentrations in the North Pacific transition zone. Dissolved GBT had maximum uptake rates of 0.36 and 0.56 nM hr -1 and half-saturation constants of 79 and 11 nM in the high nitrate and low nitrate stations, respectively. GBT taken into cells was predominantly retained as an untransformed compatible solute. A portion of GBT was transformed into other metabolites, through characterized and uncharacterized pathways. Where nitrate was scarce, GBT was primarily catabolized via the demethylation to glycine. Resulting metabolites were used to build protein biomass, and remineralized ammonia was re-assimilated into cells. Gene expression data from this region show that bacteria, especially SAR11, are the dominant organisms expressing the demethylation genes. Where nitrate concentrations were higher, more GBT was used for choline synthesis. Our data highlight undiscussed metabolic pathways and potential routes of microbial metabolite exchange.
Institute:University of Washington
Department:School of Oceanography
Laboratory:Ingalls Lab
Last Name:Kumler
First Name:William
Address:1501 NE Boat St, Seattle, WA, 98105, USA
Email:wkumler@uw.edu
Phone:2062216732
Funding Source:Simons Collaboration on Ocean Processes and Ecology, NSF

Subject:

Subject ID:SU002089
Subject Type:Other organism
Subject Species:Natural mixed marine microbial community

Factors:

Subject type: Other organism; Subject species: Natural mixed marine microbial community (Factor headings shown in green)

mb_sample_id local_sample_id Sample type Dilution factor Experiment number Timepoint
SA187880200605_Blk_GBTFate1MBlk_B_20200607110426_neg_HILICBlank 1 1 NA
SA187881200605_Blk_GBTFate1MBlk-neg_A_neg_HILICBlank 1 1 NA
SA187882200612_Blk_GBTFate1MBlk-IS_A_pos_CYANOBlank 1 1 NA
SA187883200605_Blk_GBTFate1MBlk-IS_B_neg_HILICBlank 1 1 NA
SA187884200612_Blk_GBTFate1MBlk-pos_A_pos_CYANOBlank 1 1 NA
SA187885200605_Blk_GBTFate1MBlk-IS_A_neg_HILICBlank 1 1 NA
SA187886200605_Blk_GBTFate1MBlk-IS_A_pos_HILICBlank 1 1 NA
SA187887200612_Blk_GBTFate1MBlk-IS_B_pos_CYANOBlank 1 1 NA
SA187888200612_Blk_GBTFate1MBlk-pos_B_pos_CYANOBlank 1 1 NA
SA187889200605_Blk_GBTFate1MBlk-pos_A_pos_HILICBlank 1 1 NA
SA187890200605_Blk_GBTFate1MBlk-pos_B_pos_HILICBlank 1 1 NA
SA187891200605_Blk_GBTFate1MBlk-IS_B_pos_HILICBlank 1 1 NA
SA187846190730_Blk_Blk_2Blank 1 - NA
SA187847190730_Blk_Blk_19Blank 1 - NA
SA187848190730_Blk_Blk_18Blank 1 - NA
SA187849190730_Blk_Blk_20Blank 1 - NA
SA187850190730_Blk_Blk_21Blank 1 - NA
SA187851190730_Blk_Blk_24Blank 1 - NA
SA187852190730_Blk_Blk_23Blank 1 - NA
SA187853190730_Blk_Blk_17Blank 1 - NA
SA187854190730_Blk_Blk_15Blank 1 - NA
SA187855190730_Blk_Blk_11Blank 1 - NA
SA187856190730_Blk_Blk_10Blank 1 - NA
SA187857190730_Blk_Blk_1Blank 1 - NA
SA187858190730_Blk_Blk_12Blank 1 - NA
SA187859190730_Blk_Blk_13Blank 1 - NA
SA187860190730_Blk_Blk_25Blank 1 - NA
SA187861190730_Blk_Blk_14Blank 1 - NA
SA187862190730_Blk_Blk_16Blank 1 - NA
SA187863190730_Blk_Blk_22Blank 1 - NA
SA187864190730_Blk_Blk_5Blank 1 - NA
SA187865190730_Blk_Blk_26Blank 1 - NA
SA187866190730_Blk_Blk_34Blank 1 - NA
SA187867190730_Blk_Blk_6Blank 1 - NA
SA187868190730_Blk_Blk_7Blank 1 - NA
SA187869190730_Blk_Blk_9Blank 1 - NA
SA187870190730_Blk_Blk_8Blank 1 - NA
SA187871190730_Blk_Blk_33Blank 1 - NA
SA187872190730_Blk_Blk_4Blank 1 - NA
SA187873190730_Blk_Blk_28Blank 1 - NA
SA187874190730_Blk_Blk_32Blank 1 - NA
SA187875190730_Blk_Blk_29Blank 1 - NA
SA187876190730_Blk_Blk_27Blank 1 - NA
SA187877190730_Blk_Blk_3Blank 1 - NA
SA187878190730_Blk_Blk_31Blank 1 - NA
SA187879190730_Blk_Blk_30Blank 1 - NA
SA187895200605_Poo_TruePooGBT_Half6neg_neg_HILICPooled 0.5 NA NA
SA187896200605_Poo_TruePooGBT_Half2_neg_HILICPooled 0.5 NA NA
SA187897200605_Poo_TruePooGBT_Half3_neg_HILICPooled 0.5 NA NA
SA187898200605_Poo_TruePooGBT_Half4_neg_HILICPooled 0.5 NA NA
SA187899200605_Poo_TruePooGBT_Half1_pos_HILICPooled 0.5 NA NA
SA187900200605_Poo_TruePooGBT_Half3_pos_HILICPooled 0.5 NA NA
SA187901200612_Poo_TruePooGBT_Half4_pos_CYANOPooled 0.5 NA NA
SA187902200612_Poo_TruePooGBT_Half3_pos_CYANOPooled 0.5 NA NA
SA187903200612_Poo_TruePooGBT_Half2_pos_CYANOPooled 0.5 NA NA
SA187904200612_Poo_TruePooGBT_Half1_pos_CYANOPooled 0.5 NA NA
SA187905200612_Poo_TruePooGBT_Half5_pos_CYANOPooled 0.5 NA NA
SA187906200605_Poo_TruePooGBT_Half6pos_pos_HILICPooled 0.5 NA NA
SA187907200605_Poo_TruePooGBT_Half1_neg_HILICPooled 0.5 NA NA
SA187908200605_Poo_TruePooGBT_Half4_pos_HILICPooled 0.5 NA NA
SA187909200605_Poo_TruePooGBT_Half5_pos_HILICPooled 0.5 NA NA
SA187910200605_Poo_TruePooGBT_Half2_pos_HILICPooled 0.5 NA NA
SA187911200605_Poo_TruePooGBT_Half5_neg_HILICPooled 0.5 NA NA
SA187892190730_Poo_TruePooGBT-K_Half2Pooled 0.5 - NA
SA187893190730_Poo_TruePooGBT-K_Half1Pooled 0.5 - NA
SA187894190730_Poo_TruePooGBT-K_Half3Pooled 0.5 - NA
SA187915200605_Poo_TruePooGBT_Full5_pos_HILICPooled 1 NA NA
SA187916200605_Poo_TruePooGBT_Full4_pos_HILICPooled 1 NA NA
SA187917200605_Poo_TruePooGBT_Full6pos_pos_HILICPooled 1 NA NA
SA187918200605_Poo_TruePooGBT_Full4_neg_HILICPooled 1 NA NA
SA187919200605_Poo_TruePooGBT_Full3_pos_HILICPooled 1 NA NA
SA187920200605_Poo_TruePooGBT_Full2_neg_HILICPooled 1 NA NA
SA187921200605_Poo_TruePooGBT_Full1_pos_HILICPooled 1 NA NA
SA187922200605_Poo_TruePooGBT_DDAneg_neg_HILICPooled 1 NA NA
SA187923200605_Poo_TruePooGBT_Full1_neg_HILICPooled 1 NA NA
SA187924200605_Poo_TruePooGBT_DDApos_pos_HILICPooled 1 NA NA
SA187925200605_Poo_TruePooGBT_Full5_neg_HILICPooled 1 NA NA
SA187926200605_Poo_TruePooGBT_Full2_pos_HILICPooled 1 NA NA
SA187927200605_Poo_TruePooGBT_Full3_neg_HILICPooled 1 NA NA
SA187928200612_Poo_TruePooGBT_Full3_pos_CYANOPooled 1 NA NA
SA187929200605_Poo_TruePooGBT_Full6neg_neg_HILICPooled 1 NA NA
SA187930200612_Poo_TruePooGBT_Full2_pos_CYANOPooled 1 NA NA
SA187931200612_Poo_TruePooGBT_Full1_pos_CYANOPooled 1 NA NA
SA187932200612_Poo_TruePooGBT-Full_DDApos35_pos_CYANOPooled 1 NA NA
SA187933200612_Poo_TruePooGBT-Full_DDApos50_pos_CYANOPooled 1 NA NA
SA187934200612_Poo_TruePooGBT_Full5_pos_CYANOPooled 1 NA NA
SA187935200612_Poo_TruePooGBT_Full4_pos_CYANOPooled 1 NA NA
SA187936200612_Poo_TruePooGBT-Full_DDApos20_pos_CYANOPooled 1 NA NA
SA187912190730_Poo_TruePooGBT-K_Full1Pooled 1 - NA
SA187913190730_Poo_TruePooGBT-K_Full2Pooled 1 - NA
SA187914190730_Poo_TruePooGBT-K_Full3Pooled 1 - NA
SA188014200612_Smp_GBTFate1MT0-IS_A_pos_CYANOSample 1 1 -
SA188015200612_Smp_GBTFate1MT0-IS_B_pos_CYANOSample 1 1 -
SA188016200612_Smp_GBTFate1MT0-IS_C_pos_CYANOSample 1 1 -
SA188017200612_Smp_GBTFate1MT0-pos_B_pos_CYANOSample 1 1 -
SA188018200612_Smp_GBTFate1MT0-pos_C_pos_CYANOSample 1 1 -
SA188019200612_Smp_GBTFate1MT0-pos_A_pos_CYANOSample 1 1 -
SA188020200605_Smp_GBTFate1MT0-pos_B_pos_HILICSample 1 1 -
SA188021200605_Smp_GBTFate1MT0-IS_C_pos_HILICSample 1 1 -
SA188022200605_Smp_GBTFate1MT0-IS_B_pos_HILICSample 1 1 -
Showing page 1 of 5     Results:    1  2  3  4  5  Next     Showing results 1 to 100 of 433

Collection:

Collection ID:CO002082
Collection Summary:Samples were collected aboard the R/V Kilo Moana in April, 2019. Experiments were conducted at two stations: station 4 at 41°40.85’ N and 158°3.01’ W, and station 5 at 37°0.21’ N and 158°0.20’ W, respectively. Water for samples of the in situ conditions and for the incubation experiments were collected with Niskin bottles attached to the CTD from 15 m water depth, which was within the surface mixed layer, in the morning.
Sample Type:Suspended Marine Particulate Matter
Collection Method:CTD Niskin Bottle
Collection Location:North Pacific
Volumeoramount Collected:2L-10L

Treatment:

Treatment ID:TR002101
Treatment Summary:In order to determine the kinetics of GBT (glycine betaine) uptake, whole seawater was spiked with varying concentrations of 13C5, 15N1-GBT and incubated for 25–42 minutes. Water was collected into 2 L bottles around 8:00 am local time for both experiments. In order to minimize the biological transformation of 13C5, 15N1-GBT into other molecules and to limit the induction of enzymatic activity, the incubation time with 13C5, 15N1-GBT was kept short. The short incubation time necessitated that samples be spiked throughout the course of the day since only six samples could be processed at a time. Before and after the addition of 13C5, 15N1-GBT, bottles were kept in flow-through incubators with blue shading to be at in situ temperature and approximately mixed layer light conditions. Samples were spiked to have final concentrations of 0, 2, 5, 10, 50, 200, or 2000 nM 13C5, 15N1-GBT. Triplicates of each 13C5, 15N1-GBT concentration were processed for both experiments, with replicates spread throughout the sampling period. After incubation with the spiked molecule, seawater was filtered onto 47 mm diameter, 0.2 µm pore size PTFE (Omnipore) filters using a peristaltic pump, polycarbonate filter holder, and Masterflex PharMed BPT tubing (Cole-Parmer). Filtering time was 10–42 minutes with an average time of 22 minutes. Experimental blanks were collected for each spike concentration during the northern experiment by collecting filtrate from one replicate of each treatment and re-filtering filtrate onto a new filter. This provided a measure of dissolved organic compounds adsorbed onto the filter during processing. Filters were frozen in liquid nitrogen immediately after filtration and stored at -80 °C until the filters were extracted using the metabolite extraction method described in Boysen et al. (2018). For the GBT fate experiments, two time course incubation experiments were performed, one at each of the stations described above. For each experiment, 2 L bottles were filled with seawater collected with the CTD from 15 m depth (within the mixed layer) at approximately 6:00 am local time. All 2 L bottles were spiked with 500 nM 13C5, 15N1-GBT and incubated in temperature-controlled incubators at 10 °C and 14 °C for the north and south experiments, respectively. Samples for the initial timepoint (T0) were filtered directly after being spiked, resulting in actual incubation times of approximately 20 minutes. At each time point triplicate 2 L bottles were sampled for analysis of bacterial and picophytoplankton abundance and biomass via flow cytometry, metabolites, and total hydrolyzable amino acids. Timepoints sampled in the north experiment were 0, 4.5, 9, 12.5, 36, 50, and 98 hours. Timepoints sampled in the south experiment were 0, 6, 13, 25, 51, and 100 hours. For all samples, incubation time was calculated by taking the difference between the time the bottle was spiked and the midpoint time of sample filtration.
Treatment:Isotopically labeled glycine betaine additions to natural seawater
Treatment Compound:13C5, 15N1 GBT (glycine betaine labeled with 5 carbon-13 atoms and one nitrogen-15 atom)
Treatment Dosevolume:0, 2, 5, 10, 50, 200, 2000 nM; 500nM
Treatment Doseduration:25-42 minutes; 0, 4.5, 6, 9,12.5, 13, 25, 36, 50, 51, 98, 100 hours

Sample Preparation:

Sampleprep ID:SP002095
Sampleprep Summary:Polar and nonpolar metabolites were extracted using a modified Bligh−Dyer extraction using 1:1 methanol/water (aqueous phase) and dichloromethane (organic phase). Methodological blanks were extracted and analyzed along with each sample set. Each sample was aliquotted into two vials and isotope-labeled internal standards were added either before or after the extraction to one vial for all samples, blanks, and pooled samples. To evaluate the effect of obscuring variation due to different matrix strengths and analytical drift, pooled samples were run at both full and half concentration (diluted with water) at least three times throughout a sample set.
Processing Storage Conditions:On ice
Extraction Method:Bligh-Dyer
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003271 AN003272 AN003273 AN003274
Analysis type MS MS MS MS
Chromatography type HILIC HILIC HILIC Reversed phase
Chromatography system Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class Waters Acquity I-Class
Column SeQuant ZIC-HILIC (150 x 2.1mm,5um) SeQuant ZIC-HILIC (150 x 2.1mm,5um) SeQuant ZIC-HILIC (150 x 2.1mm,5um) Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI
MS instrument type Triple quadrupole Orbitrap Orbitrap Orbitrap
MS instrument name Waters Xevo TQ-S Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE POSITIVE
Units nmol/L Peak area Peak area Peak area

Chromatography:

Chromatography ID:CH002415
Chromatography Summary:See protocol wkumler_20211201_100602_PR_CH_CH_Ingalls_Lab_LC_Methods.txt
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Chromatography Type:HILIC
  
Chromatography ID:CH002416
Chromatography Summary:See protocol wkumler_20211201_100602_PR_CH_CH_Ingalls_Lab_LC_Methods.txt
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003043
Analysis ID:AN003271
Instrument Name:Waters Xevo TQ-S
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:See protocol PR_MS_Ingalls_Lab_MS_Methods_TQS.txt
Ion Mode:POSITIVE
  
MS ID:MS003044
Analysis ID:AN003272
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See protocol PR_MS_Ingalls_Lab_MS_Methods_GBT.txt
Ion Mode:POSITIVE
  
MS ID:MS003045
Analysis ID:AN003273
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See protocol PR_MS_Ingalls_Lab_MS_Methods_GBT.txt
Ion Mode:NEGATIVE
  
MS ID:MS003046
Analysis ID:AN003274
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See protocol PR_MS_Ingalls_Lab_MS_Methods_GBT.txt
Ion Mode:POSITIVE
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